We investigated the Fourier-transformed mid-infrared (MIR) and near-infrared (NIR) spectroscopic properties of mycorrhizal (M) and non-mycorrhizal (NM) carrot roots with the goal of finding infrared markers for colonization by arbuscular mycorrhizal (AM) fungi. The roots were cultured with or without the AM fungus <i>Glomus intraradices</i> under laboratory conditions. A total of 50 M and NM samples were produced after pooling subsamples. The roots were dried, ground, and scanned separately for the NIR and MIR analyses. The root samples were analyzed for fatty acid composition in order to confirm mycorrhizal infection and to determine the presence of fatty acid markers. Besides the roots, fatty acid standards, pure cultures of saprophytic fungi, and chitin were also scanned in order to identify spectral bands likely to be found in M samples. Principal components analysis (PCA) was used to illustrate spectral differences between the M and NM root samples. The NIR analysis achieved good resolution with the raw spectral data and no pretreatment was needed to obtain good resolution in the PCA analysis of the NIR data. Standard normal variate and detrending pretreatment improved the resolution between M and NM in the MIR range. The PCA loadings and/or the spectral subtraction of selected samples showed that M roots are characterized by absorbances at or close to 400 cm<sup>−1</sup>, 1100–1170 cm<sup>−1</sup>, 1690 cm<sup>−1</sup>, 2928 cm<sup>−1</sup>, and 5032 cm<sup>−1</sup>. The NM samples had characteristic absorbances at or near 1734 cm<sup>−1</sup>, 3500 cm<sup>−1</sup>, 4000 cm<sup>−1</sup>, 4389 cm<sup>−1</sup>, and 4730 cm<sup>−1</sup>. Some of the bands that differentiate M from NM roots are prominent in the spectra of pure fungal cultures, chitin, and fatty acids. Our results show that mycorrhizal and nonmycorrhizal root tissues can be differentiated via MIR and NIR spectra with the advantage that the same samples can then be used for other analyses.

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